nf-coreGPT-AI-powered Nextflow pipeline assistance.

Example

nf-coreGPT helps users design and implement Nextflow pipelines from scratch or optimize existing ones. It can provide code snippets, explain specific DSL2 syntax features, and suggest best practices.

Scenario

A user needs to create a pipeline for RNA-seq data analysis that includes quality control, alignment, and differential expression analysis. nf-coreGPT provides the necessary steps and code examples for implementing each stage, ensuring the pipeline is modular, reproducible, and scalable.

Example

When users encounter errors or unexpected behavior in their pipelines, nf-coreGPT can diagnose the issues based on error messages and logs, offering potential solutions or workarounds.

Scenario

A pipeline fails to execute on a specific process, and the user receives a cryptic error message. nf-coreGPT analyzes the error, identifies that it is due to a memory allocation issue, and advises on how to adjust the resource requirements in the Nextflow configuration file.

Example

nf-coreGPT can guide users in configuring their pipelines to run efficiently on different computing environments, including local machines, HPC clusters, and cloud platforms.

Scenario

A user is transitioning a pipeline from a local environment to a cloud-based infrastructure like AWS. nf-coreGPT explains how to modify the pipeline's configuration to use cloud-specific executors, such as AWS Batch, and optimize costs by managing resource allocation effectively.